Creating a new tutorial - Creating Interactive Galaxy Tours
- What is a Interactive Galaxy Tour?
- How can we create an Interactive Tour?
- Creating a Galaxy tour from scratch
- Deploying and running a tour
time Time estimation: 15 minutesSupporting Materials
Galaxy is a great solution to train the bioinformatics concepts:
- numerous bioinformatics tools are available (almost 5,000 in the ToolShed)
- it can be used by people without any computer science skills
- it trains to use technology, outlining available resources and efforts that have made them accessible to researchers
- it is scalable
In 2016, the Galaxy Training Network decide to set up a new infrastructure for delivering easily Galaxy related training material. The idea was to develop something open and online based on a community effort, as most of the time in Galaxy.
We take inspiration from Software Carpentry. We collected everything on a GitHub repository: https://github.com/galaxyproject/training-material . We decided a structure based on tutorials with hands-on, fitting both for online self-training but also for workshops, grouped in topics. Each tutorial follows the same structure and comes with a technical support to be able to run.
In this tutorial, you will understand how to design and develop a new tutorial fitting in this training material repository. As doing helps to understand, we will develop a small tutorial to explain BLAST with the full infrastructure to be able to run this tutorial anywhere.
In this tutorial, we will deal with:
A Galaxy Interactive Tour
A Galaxy Interactive Tour is a way to go through an entire analysis, step by step inside Galaxy in an interactive and explorative way. It is a great pedagogic way to run the tutorial directly inside Galaxy.
A tour is a YAML file like:
id: galaxy_ui name: Galaxy UI description: A gentle introduction to the Galaxy User Interface title_default: "Welcome to Galaxy" steps: - title: "Welcome to Galaxy" content: "This short tour will guide you through Galaxy's user interface.<br> You can navigate with your arrow keys and leave the tour at any time point with 'Escape' or the 'End tour' button." backdrop: true - title: "Upload your data" element: ".upload-button" intro: "Galaxy supports many ways to get in your data.<br> Use this button to upload your data." position: "right" postclick: - ".upload-button"
- at the top some metadata related to the Tour:
id: ID of the tour
name: name of the tour
description: a short description of the tour
title_default: a title
several steps corresponding to the different boxes
Each step is beginning with a dash
-and with possible arguments
Header of each step-container
Text that is shown to the user
JQuery Selector of the element you want to describe / click
Placement of the text box relative to the selected element
Elements that receive a click() event before (
preclick) or after (
postclick) the step is shown
Text to insert if element is a text box (e.g. tool search or upload)
true/false: Show a dark backdrop behind the popover and its element, highlighting the current step
The YAML file of a tour can be integrated in a Galaxy instance by placing the YAML file in the
config/plugins/tours directory of the Galaxy code and restarting the Galaxy instance
Creating a Galaxy Interactive Tour
A Web browser plugin is available to help the creation and the test (on the fly) of an interactive tour.
hands_on Hands-on: Install and start the plugin
We can now create easily a Galaxy Interactive Tour and test it on the fly.
hands_on Hands-on: Create a Galaxy Interactive Tour
- Create a Galaxy Interactive Tour for “BLAST” tutorial
- Test it with the plugin
- Copy the YAML content and add it to a file
- Add the file to the
toursdirectory of the tutorial
- Test it on a local Galaxy instance
keypoints Key points
- The Interactive Tours are a good training object for self-learning at its own speed
- It is now easy to create an Interactive Tour and test it
congratulations Congratulations on successfully completing this tutorial!
Developing GTN training materialThis tutorial is part of a series to develop GTN training material, feel free to also look at:
- Overview of the Galaxy Training Material
- Contributing with GitHub via command-line
- Contributing with GitHub via its interface
- Creating a new tutorial
- Creating a new tutorial - Creating Interactive Galaxy Tours
- Creating a new tutorial - Defining the technical infrastructure
- Creating a new tutorial - Slides
- Creating a new tutorial - Writing content in Markdown
- Generating PDF artefacts of the website
- Including a new topic
- Running the Galaxy Training material website locally
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